TY - JOUR AU - Kim, Sangwoo AU - Jeong, Kyowon AU - Bhutani, Kunal AU - Lee, Jeong Ho AU - Patel, Anand AU - Scott, Eric AU - Nam, Hojung AU - Lee, Hayan AU - Gleeson, Joseph G. AU - Bafna, Vineet PY - 2013 DA - 2013/08/29 TI - Virmid: accurate detection of somatic mutations with sample impurity inference JO - Genome Biology SP - R90 VL - 14 IS - 8 AB - Detection of somatic variation using sequence from disease-control matched data sets is a critical first step. In many cases including cancer, however, it is hard to isolate pure disease tissue, and the impurity hinders accurate mutation analysis by disrupting overall allele frequencies. Here, we propose a new method, Virmid, that explicitly determines the level of impurity in the sample, and uses it for improved detection of somatic variation. Extensive tests on simulated and real sequencing data from breast cancer and hemimegalencephaly demonstrate the power of our model. A software implementation of our method is available at http://sourceforge.net/projects/virmid/. SN - 1474-760X UR - https://doi.org/10.1186/gb-2013-14-8-r90 DO - 10.1186/gb-2013-14-8-r90 ID - Kim2013 ER -